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<h2><a name='types'>ROI types</a></h2>
<p>
There are four types of ROI that can be used for tracking:
</p>
<dl>
  <dt>seed</dt>
  <dd>the tracking algorithm will initiate tracks from random location within these regions.</dd>
  <dt>include</dt>
  <dd><em>target</em> ROIs: tracks generated by the algorithm will need to pass through the ROI; tracks that do not enter the ROI will be discarded.</dd>
  <dt>exclude</dt>
  <dd>tracks that enter these ROIs will immediately be discarded.</dd>
  <dt>mask</dt>
  <dd>tracks must be contained within these ROIs; track will be terminated (but <em>not</em> discarded) as soon as they leave the ROI.</dd>
</dl>

<p class=sep><a href="#top">top</a></p>
<h2><a name='define'>Defining ROIs</a></h2>
<p>
ROIs can be specified as spherical regions, or as a mask image.
</p>
<h3><a name='sphere'>Spherical ROIs</a></h3>
<p>
These are best defined using MRView. 
For example:
</p>
<pre>
&gt; <b><a href='../commands/mrview.html'>mrview</a> anat.mif</b>
</pre>
<p>
Set MRView to display cross-hairs on the current focus, using the 'View-&gt;Show Focus' menu:
</p>
<img src=focus.png>
<p>
Place the cross-hairs in the desired seed location, and read off the real-world position from the statusbar, 
as shown below:
</p>
<img src=position.png>
<p>
The ROI can then be specified using this position, along with its desired radius.
</p>

<h3><a name='mask'>Mask ROIs</a></h3>
<p>
Regions of interest can also be specified in the form of mask images. 
In this case, the set of voxels with intensities greater than 0.5 constitutes the ROI.
The 'ROI analysis' of MRView can be used to define such ROIs (see <a href='../general/mrview.html#roi'>ROI analysis</a> for details). 



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